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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-16, 11:00 based on data in: /home/chengxin/pmultiqctest/test_phos


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 4/4 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.mzML111111
        SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.mzML211111
        SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.mzML311222
        SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.mzML411222

        HeatMap

        This plot shows the pipeline performance overview

        This plot shows the pipeline performance overview. Some metrics are calculated.

        • Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
        • Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
        • Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
        • Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
        • Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
        • Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
        • Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
        • Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
        loading..

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 5/5 columns.
        Total MS/MS SpectralTotal MS/MS Spectral IdentifiedIdentified MS/MS Spectral CoverageTotal Peptide IdentifiedTotal Protein IdentifiedTotal Protein Quantified
        12870
        1157
        8.99%
        196
        106
        93

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 4/4 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.mzML
        1
        1
        1
        131
        63
        102
        49
        SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.mzML
        1
        1
        1
        127
        57
        101
        43
        SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.mzML
        2
        2
        1
        240
        150
        205
        67
        SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.mzML
        2
        2
        1
        232
        130
        203
        74

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Spectra Tracking

        This plot shows the quantms pipeline mzML tracking

        This table shows the changes in the number of spectra corresponding to each input file during the pipeline operation. And the number of peptides finally identified is obtained from the PSM table in the mzTab file. You can also remove the decoy with the remove_decoy parameter.:

        • MS1_Num: The number of MS1 spectra extracted from mzMLs
        • MS2_Num: The number of MS2 spectra extracted from mzMLs
        • MSGF: The Number of spectra identified by MSGF search engine
        • Comet: The Number of spectra identified by Comet search engine
        • Final result of spectra: extracted from PSM table in mzTab file
        • Final result of Peptides: extracted from PSM table in mzTab file
        Showing 4/4 rows and 6/6 columns.
        Spectra FileMS1_NumMS2_NumFinal result of spectraCometFinal result of PeptidesMSGF
        SF_200217_pPeptideLibrary_pool1_HCDOT_rep1.mzML
        4368
        3097
        213
        1497
        55
        1539
        SF_200217_pPeptideLibrary_pool1_HCDOT_rep2.mzML
        4449
        2868
        218
        1440
        47
        1440
        SF_200217_pPeptideLibrary_pool2_HCDOT_rep1.mzML
        4190
        3538
        SF_200217_pPeptideLibrary_pool2_HCDOT_rep2.mzML
        4303
        3367

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Oversampling Distribution

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.

        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.

                    * Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
        
        loading..

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Click distribution to switch to bar plots.
        Showing 50/50 rows and 8/8 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage Intensity1212
        1
        IPI00004344_1
        .(Acetyl)AVGM(Oxidation)PSPVS(Phospho)PK
        0.78253
        6.15416
        6.15416
        0.00000
        2
        IPI00000685_1;IPI00000685_2
        .(Acetyl)AYT(Phospho)HQVVTR
        0.97376
        6.70114
        0.00000
        6.70114
        3
        IPI00004497_4
        .(Acetyl)DALVSGALESTK
        0.99926
        7.22690
        0.00000
        7.22690
        4
        sp|OVAL_CHICK|
        .(Acetyl)DEDTQ(Deamidated)AMPFRVTEQ(Deamidated)ESK
        0.89673
        6.17078
        0.00000
        6.17078
        5
        sp|TRFL_HUMAN|
        .(Acetyl)DEY(Phospho)ELLC(Carbamidomethyl)PDNT(Phospho)RK
        0.84262
        6.18842
        0.00000
        6.18842
        6
        IPI00025076
        .(Acetyl)DIYSTDYY(Phospho)R
        0.87499
        6.42564
        0.00000
        6.42564
        7
        IPI00025076
        .(Acetyl)DIYSTDYYR
        0.99415
        6.26565
        0.00000
        6.26565
        8
        KKA1_ECOLX
        .(Acetyl)DN(Deamidated)VGQSGATIY(Phospho)R
        0.53566
        6.92845
        0.00000
        6.92845
        9
        IPI00018597_4;IPI00018597_5;IPI00018597_6
        .(Acetyl)EALPM(Oxidation)DT(Phospho)EVYESPYADPEEIRPK
        0.99997
        6.86105
        0.00000
        6.86105
        10
        IPI00328149_1;IPI00328149_2
        .(Acetyl)FGES(Phospho)DTENQNNK
        0.81483
        6.22706
        6.22706
        0.00000
        11
        IPI00328149_1;IPI00328149_2
        .(Acetyl)FGESDTENQNNK
        0.99398
        6.19838
        6.19838
        0.00000
        12
        IPI00293613
        .(Acetyl)FGS(Phospho)LTM(Oxidation)DGGLR
        0.99283
        5.51326
        0.00000
        5.51326
        13
        IPI00041176_1;IPI00041176_2
        .(Acetyl)FSDQAGPAIPTSNSY(Phospho)SK
        0.95220
        6.70932
        0.00000
        6.70932
        14
        IPI00041176_1;IPI00041176_2
        .(Acetyl)FSDQAGPAIPTSNSYS(Phospho)K
        0.99998
        6.58472
        0.00000
        6.58472
        15
        sp|TRFL_HUMAN|
        .(Acetyl)GGSFQ(Deamidated)LN(Deamidated)ELQGLK
        0.50755
        6.83628
        0.00000
        6.83628
        16
        sp|TRFL_HUMAN|
        .(Acetyl)GGSFQ(Deamidated)LNELQ(Deamidated)GLK
        0.66741
        6.71325
        0.00000
        6.71325
        17
        IPI00016932_2
        .(Acetyl)GLPSDY(Phospho)GR
        0.99115
        6.10675
        0.00000
        6.10675
        18
        IPI00000878_1
        .(Acetyl)GQEY(Phospho)LILEK
        0.96516
        5.93446
        5.93446
        0.00000
        19
        sp|BGAL_ECOLI|
        .(Acetyl)IENGLLLLNGK
        0.72668
        5.87709
        0.00000
        5.87709
        20
        IPI00018597_2
        .(Acetyl)IKS(Phospho)YSFPK
        0.74101
        6.87294
        6.87294
        0.00000
        21
        IPI00013905
        .(Acetyl)IPLIKS(Phospho)HN(Deamidated)DFVAILDLPEGEHQYK
        0.95616
        6.58894
        0.00000
        6.58894
        22
        sp|CO5_HUMAN|
        .(Acetyl)KQT(Phospho)AC(Carbamidomethyl)K
        0.93033
        6.60316
        0.00000
        6.60316
        23
        sp|BGAL_ECOLI|
        .(Acetyl)KWLS(Phospho)LPGETR
        0.95548
        7.60070
        0.00000
        7.60070
        24
        sp|KRHB1_HUMAN|
        .(Acetyl)LC(Carbamidomethyl)EGIGAVNVC(Carbamidomethyl)VSS(Phospho)S(Phospho)R
        0.65043
        6.24273
        0.00000
        6.24273
        25
        sp|CO5_HUMAN|
        .(Acetyl)LHMKTLLPVS(Phospho)K
        0.86040
        7.07578
        0.00000
        7.07578
        26
        IPI00220409
        .(Acetyl)LPLT(Phospho)RSHNN(Deamidated)FVAILDLPEGEHQYK
        0.62478
        5.67943
        0.00000
        5.67943
        27
        sp|K1HB_HUMAN|
        .(Acetyl)LPSN(Deamidated)PC(Carbamidomethyl)ATTN(Deamidated)AC(Carbamidomethyl)EK
        0.91259
        6.02140
        0.00000
        6.02140
        28
        IPI00009334_1;IPI00009334_2;IPI00009334_3
        .(Acetyl)LS(Phospho)S(Phospho)TSLASGHSVR
        0.99966
        7.69571
        0.00000
        7.69571
        29
        IPI00009334_1;IPI00009334_2;IPI00009334_3
        .(Acetyl)LSS(Phospho)TSLASGHSVR
        0.99700
        6.59824
        0.00000
        6.59824
        30
        IPI00009334_1;IPI00009334_2;IPI00009334_3
        .(Acetyl)LSST(Phospho)SLASGHSVR
        0.98858
        7.16794
        0.00000
        7.16794
        31
        sp|CO5_HUMAN|
        .(Acetyl)M(Oxidation)PITYDN(Deamidated)GFLFIHT(Phospho)DK
        0.75080
        5.03148
        0.00000
        5.03148
        32
        IPI00216378_1
        .(Acetyl)NFSAAKS(Phospho)LLNK
        0.63183
        6.74559
        6.74559
        0.00000
        33
        IPI00219628
        .(Acetyl)NIDQS(Phospho)EFEGFSFVNSEFLKPEVK
        0.99979
        6.00213
        0.00000
        6.00213
        34
        IPI00025830
        .(Acetyl)PDHPGTPPHK
        0.99986
        6.41457
        0.00000
        6.41457
        35
        sp|K1H2_HUMAN|
        .(Acetyl)PELC(Carbamidomethyl)LGYVC(Carbamidomethyl)QPM(Oxidation)AC(Carbamidomethyl)LPSVC(Carbamidomethyl)LPT(Phospho)TFR
        0.95706
        5.78911
        0.00000
        5.78911
        36
        sp|TRY1_BOVIN|
        .(Acetyl)PGVY(Phospho)TKVC(Carbamidomethyl)N(Deamidated)YVSWIK
        0.73388
        5.78037
        0.00000
        5.78037
        37
        IPI00216969_13;IPI00216969_5
        .(Acetyl)PS(Phospho)QSPSQEAAGEAVLGAK
        0.99998
        6.26511
        6.26511
        0.00000
        38
        IPI00465017
        .(Acetyl)PT(Phospho)T(Phospho)GVILPSGNTLRVK
        0.73097
        7.43795
        0.00000
        7.43795
        39
        sp|TAU_HUMAN|
        .(Acetyl)PVSRVPQLK
        0.99605
        6.36655
        0.00000
        6.36655
        40
        sp|CAH2_HUMAN|
        .(Acetyl)QSPVDIDTHTAKY(Phospho)DPS(Phospho)LK
        0.94327
        7.38871
        0.00000
        7.38871
        41
        KKA1_ECOLX
        .(Acetyl)S(Phospho)HIQRETSC(Carbamidomethyl)SR
        0.94059
        6.46130
        0.00000
        6.46130
        42
        IPI00220409
        .(Acetyl)S(Phospho)HNNFVAILDLPEGEHQYK
        0.85645
        6.03620
        0.00000
        6.03620
        43
        IPI00329488_10;IPI00329488_16;IPI00329488_3
        .(Acetyl)S(Phospho)SSFREM(Oxidation)ENQPHK
        0.64308
        6.79387
        0.00000
        6.79387
        44
        IPI00012318_2
        .(Acetyl)SEVAVLS(Phospho)PEKAEN(Deamidated)DDTYKDDVNHNQK
        0.99904
        5.94523
        0.00000
        5.94523
        45
        IPI00012318_2
        .(Acetyl)SEVAVLSPEKAEN(Deamidated)DDTYK
        0.72532
        5.17679
        0.00000
        5.17679
        46
        IPI00012318_2
        .(Acetyl)SEVAVLSPEKAEN(Deamidated)DDTYKDDVN(Deamidated)HNQK
        0.49463
        5.65186
        0.00000
        5.65186
        47
        KKA1_ECOLX
        .(Acetyl)SHIQRET(Phospho)SC(Carbamidomethyl)SR
        0.97195
        6.41236
        0.00000
        6.41236
        48
        sp|CO5_HUMAN|
        .(Acetyl)SKRMPIT(Phospho)Y(Phospho)DNGFLFIHT(Phospho)DK
        0.91283
        7.46336
        0.00000
        7.46336
        49
        sp|ANT3_HUMAN|
        .(Acetyl)SLNPNRVTFKANR
        0.79347
        6.86174
        0.00000
        6.86174
        50
        IPI00329488_15;IPI00329488_2;IPI00329488_5;IPI00329488_7;IPI00329488_9
        .(Acetyl)SNS(Phospho)TSSM(Oxidation)SSGLPEQDR
        0.99727
        6.84779
        0.00000
        6.84779
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.Click distribution to switch to bar plots.
        Showing 50/50 rows and 6/6 columns.
        ProteinNamePeptides_NumberAverage Intensity1212
        IPI00000685_1;IPI00000685_2
        4
        9.69112
        0.00000
        9.69112
        IPI00000878_1
        3
        9.41498
        9.41498
        0.00000
        IPI00000878_3
        4
        8.67796
        0.00000
        8.67796
        IPI00003431
        2
        8.96712
        8.96712
        0.00000
        IPI00004344_1
        3
        8.97421
        8.97421
        0.00000
        IPI00004344_2
        2
        6.56522
        6.56522
        0.00000
        IPI00004497_1;IPI00004497_10
        3
        8.92674
        8.92674
        0.00000
        IPI00004497_3;IPI00004497_5
        5
        8.97475
        8.72865
        9.22085
        IPI00004497_4
        5
        8.99658
        0.00000
        8.99658
        IPI00009334_1;IPI00009334_2;IPI00009334_3
        5
        8.33972
        0.00000
        8.33972
        IPI00012318_1
        2
        8.45367
        0.00000
        8.45367
        IPI00012318_2
        10
        9.54690
        0.00000
        9.54690
        IPI00013905
        3
        8.19154
        0.00000
        8.19154
        IPI00014266
        2
        8.94431
        8.94431
        0.00000
        IPI00015287_1;IPI00015287_2;IPI00015287_3
        6
        9.01354
        9.01354
        0.00000
        IPI00016932_1;IPI00016932_3;IPI00016932_4
        2
        6.55710
        6.55710
        0.00000
        IPI00016932_2
        3
        9.21119
        0.00000
        9.21119
        IPI00018597_1;IPI00018597_3
        2
        8.14300
        7.96565
        8.32035
        IPI00018597_2
        7
        9.32868
        9.32868
        0.00000
        IPI00018597_4;IPI00018597_5;IPI00018597_6
        9
        8.98692
        0.00000
        8.98692
        IPI00022633_2
        2
        8.35816
        0.00000
        8.35816
        IPI00025076
        5
        9.09263
        0.00000
        9.09263
        IPI00025830
        7
        9.18974
        0.00000
        9.18974
        IPI00026689_1
        2
        8.09365
        8.09365
        0.00000
        IPI00029132_1
        1
        7.52374
        7.52374
        0.00000
        IPI00029132_3
        3
        9.22165
        0.00000
        9.22165
        IPI00029702_1;IPI00029702_2;IPI00029702_3
        7
        9.11874
        8.98630
        9.25118
        IPI00031016
        2
        9.44924
        0.00000
        9.44924
        IPI00039689_1;IPI00039689_4
        6
        9.42464
        0.00000
        9.42464
        IPI00041176_1;IPI00041176_2
        6
        9.49171
        0.00000
        9.49171
        IPI00145805
        2
        9.31869
        9.31869
        0.00000
        IPI00181703_1
        4
        9.46915
        0.00000
        9.46915
        IPI00216378_1
        4
        8.28739
        8.28739
        0.00000
        IPI00216378_2
        1
        6.27944
        6.27944
        0.00000
        IPI00216969_13;IPI00216969_5
        5
        7.68390
        7.68390
        0.00000
        IPI00216969_1;IPI00216969_11;IPI00216969_4
        8
        9.02776
        9.00541
        9.05012
        IPI00216969_2
        3
        8.73733
        8.73733
        0.00000
        IPI00216969_3;IPI00329488_8
        3
        7.42407
        8.60849
        6.23965
        IPI00219012_3
        1
        7.35002
        0.00000
        7.35002
        IPI00219628
        3
        8.13251
        0.00000
        8.13251
        IPI00220409
        8
        8.82423
        0.00000
        8.82423
        IPI00293613
        5
        9.05243
        0.00000
        9.05243
        IPI00298977_1;IPI00298977_2;IPI00298977_4
        1
        6.69815
        0.00000
        6.69815
        IPI00298977_3
        2
        6.75744
        6.75744
        0.00000
        IPI00298977_5;IPI00298978
        6
        9.41696
        9.37754
        9.45638
        IPI00301263
        2
        7.58323
        7.58323
        0.00000
        IPI00303797
        3
        8.61114
        0.00000
        8.61114
        IPI00328149_1;IPI00328149_2
        7
        8.06651
        8.26807
        7.86496
        IPI00329488_10;IPI00329488_16;IPI00329488_3
        11
        8.76483
        8.32522
        9.20444
        IPI00329488_11;IPI00329491
        10
        7.59974
        9.02630
        6.17317
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        CONSENSUSID ConsensusID 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        EXTRACTPSMFEATURES PSMFeatureExtractor 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FDRCONSENSUSID FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDSCORESWITCHERFORLUCIPHOR IDScoreSwitcher 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        LUCIPHORADAPTER Luciphor 1.2014Oct10
        LuciphorAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        PERCOLATOR PercolatorAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        percolator 3.05.0, Build Date Aug 31 2020 19:03:04
        PROTEOMICSLFQ ProteomicsLFQ 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        SEARCHENGINECOMET Comet 2019.01 rev. 5
        CometAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        fervent_aryabhata
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_localize,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/lfq_testdata/test_localize/test_phospho.sdrf
        outdir
        ./results_localize

        Protein database

        database
        /home/chengxin/lfq_testdata/test_localize/pools_crap_targetdecoy.fasta

        Database search

        search_engines
        comet,msgf
        instrument
        N/A

        Modification localization

        enable_mod_localization
        true
        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein inference

        protein_level_fdr_cutoff
        0.05
        psm_level_fdr_cutoff
        1.0

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        skip_post_msstats
        true
        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test PTM-localization profile
        config_profile_description
        Minimal test dataset to check pipeline function for PTM-localization, SDRF parsing and ConsensusID.

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        1h

        Generic options

        hostnames
        N/A